A5079952504- Mass Spectrometry Techniques and Applications
- Advanced Proteomics Techniques and Applications
- Mosquito-borne diseases and control
- Metabolomics and Mass Spectrometry Studies
- Viral Infections and Outbreaks Research
- Viral Infections and Vectors
- Monoclonal and Polyclonal Antibodies Research
- RNA and protein synthesis mechanisms
- Genomics and Chromatin Dynamics
- DNA Repair Mechanisms
- Cell Adhesion Molecules Research
- Microtubule and mitosis dynamics
- RNA modifications and cancer
- Cancer, Hypoxia, and Metabolism
- Genomics and Phylogenetic Studies
- Protein Tyrosine Phosphatases
- Enzyme Structure and Function
- Genetic factors in colorectal cancer
- Ocular Surface and Contact Lens
- Genetic Neurodegenerative Diseases
- RNA Research and Splicing
- Sphingolipid Metabolism and Signaling
- Antimicrobial Peptides and Activities
- T-cell and B-cell Immunology
- Analytical Chemistry and Chromatography
Agency for Science, Technology and Research
2022-2025
Institute of Molecular and Cell Biology
2022-2025
Memorial Sloan Kettering Cancer Center
2016-2023
Tri-Institutional PhD Program in Chemical Biology
2016-2021
Cornell University
2014-2020
Institute of Medical Biology
2016
Institute of Bioengineering and Nanotechnology
2016
Rockefeller University
2016
Aerobic glycolysis or the Warburg Effect (WE) is characterized by increased metabolism of glucose to lactate. It remains unknown what quantitative changes activity are necessary and sufficient for this phenotype. We developed a computational model an integrated analysis using metabolic control (MCA), metabolomics data, statistical simulations. identified confirmed novel mode regulation specific aerobic where flux through GAPDH, enzyme separating lower upper glycolysis, rate-limiting step in...
Recent advances in mass spectrometry have allowed for unprecedented characterization of human metabolism and its contribution to disease. Despite these advances, limitations metabolomics technology remain. Here, we describe a strategy that consolidates several recent improvements technology. The platform involves high-resolution Orbitrap spectrometer coupled faster scanning speeds, allowing polarity switching improved ion optics resulting enhanced sensitivity. When HILIC chromatography, are...
Significance The Smc5/6 complex plays multiple roles in DNA replication and repair. Its genome-protecting functions rely on its interaction with DNA; however, how this engages is poorly understood. We report a cryogenic electron microscopy structure of DNA-bound budding yeast complex, revealing that subunits form clamp to encircle double-helical DNA. define the multi-subunit interactions forming binding sites distributed among subunits. identify subunit transformations upon capture...
Structural maintenance of chromosomes (SMC) complexes are critical chromatin modulators. In eukaryotes, the cohesin and condensin SMC organize chromatin, while Smc5/6 complex directly regulates DNA replication repair. The molecular basis for distinct functions is poorly understood. Here, we report an integrative structural study budding yeast holo-complex using electron microscopy, cross-linking mass spectrometry, computational modeling. We show that possesses several unique features,...
Antimetabolites that affect nucleotide metabolism are frontline chemotherapy agents in several cancers and often successfully target one carbon metabolism. However, the precise mechanisms resulting determinants of their therapeutic value unknown. We show 5-fluorouracil (5-FU), a commonly used antimetabolite with varying efficacy, induces specific alterations to by disrupting pyrimidine homeostasis. An integrative metabolomics analysis cellular response 5-FU reveals intracellular uracil...
Recent development of mass spectrometer cleavable protein cross-linkers and algorithms for their spectral identification now permits large-scale cross-linking spectrometry (XL-MS). Here, we optimized the use disuccinimidyl sulfoxide (DSSO) cross-linker labeling native complexes in live human cells. We applied a generalized linear mixture model to calibrate cross-link peptide-spectra matching (CSM) scores control sensitivity specificity XL-MS. Using specific CSM score thresholds false...
Abstract Cancer cells undergo transcriptional reprogramming to drive tumor progression and metastasis. Using cancer cell lines patient-derived organoids, we demonstrate that loss of the negative elongation factor (NELF) complex inhibits breast development through downregulating epithelial-mesenchymal transition (EMT) stemness-associated genes. Quantitative multiplexed Rapid Immunoprecipitation Mass spectrometry Endogenous proteins (qPLEX-RIME) further reveals a significant rewiring...
Severe dengue infections are characterized by endothelial dysfunction shown to be associated with the secreted nonstructural protein 1 (sNS1), making it an attractive vaccine antigen and biotherapeutic target. To uncover biologically relevant structure of sNS1, we obtained infection-derived sNS1 (isNS1) from virus (DENV)-infected Vero cells through immunoaffinity purification instead recombinant (rsNS1) overexpressed in insect or mammalian cell lines. We found that isNS1 appeared as...
Over the last decades, organ transplantation has made rapid progress as a curative therapy for failure. However, adaptive immune system—alloreactive T cells and antibodies targeting human leukocyte antigens (HLA)—is leading cause of graft rejection. The presence anti-donor HLA is considered risk factor that disqualifies particular donor-recipient pair. alloantibodies are found in some long-term survivors, suggesting protective blocking function alloantibodies. Therefore, whether can have...
Metabolite profiling has been a valuable asset in the study of metabolism health and disease. However, current platforms have different limiting factors, such as labor intensive sample preparations, low detection limits, slow scan speeds, method optimization for each metabolite, inability to measure both positively negatively charged ions single experiments. Therefore, novel metabolomics protocol could advance studies. Amide-based hydrophilic chromatography enables polar metabolite analysis...
The Smc5/6 complex (Smc5/6) is important for genome replication and repair in eukaryotes. Its cellular functions are closely linked to the ATPase activity of Smc5 Smc6 subunits. This requires dimerization motor domains two SMC subunits regulated by six non-SMC (Nse1 Nse6). Among NSEs, Nse5 Nse6 form a stable subcomplex (Nse5-6) that dampens complex. However, underlying mechanisms biological significance this regulation remain unclear. Here, we address these issues using structural functional...
Abstract Quorum sensing (QS) is a crucial regulatory mechanism controlling bacterial signalling and holds promise for novel therapies against antimicrobial resistance. In Gram-positive bacteria, such as Streptococcus pneumoniae , ComA conserved efflux pump responsible the maturation secretion of peptide signals, including competence-stimulating (CSP), yet its structure function remain unclear. Here, we functionally characterize an ABC transporter with high ATP affinity determined cryo-EM...
Notch1 plays various roles in cancer development, and Notch1-induced transactivation is controlled by phosphorylation of its cleaved intracellular domain. However, it unclear whether there are phosphatases capable dephosphorylating the transmembrane/intracellular region (NTM) to regulate function. Here, we show that DUSP6 can function as a phosphatase for Notch1, thereby regulating NTM stability transcriptional activity, thus influencing colorectal (CRC) development. In human CRC cells,...
Diseases caused by flaviviruses such as dengue virus (DENV) and West Nile Virus (WNV), are a serious threat to public health. The flavivirus single-stranded RNA genome is translated into polyprotein which cleaved three structural proteins seven non-structural the viral cellular proteases. Non-structural (NS) protein 3 multifunctional that has N-terminal protease C-terminal helicase domains. NS3 requires co-factor NS2B for enzymatic activity folding. Due its essential role in replication,...
Metabolite profiling has been a valuable asset in the study of metabolism health and disease. However, current platforms have different limiting factors, such as labor intensive sample preparations, low detection limits, slow scan speeds, method optimization for each metabolite, inability to measure both positively negatively charged ions single experiments. Therefore, novel metabolomics protocol could advance studies. Amide-based hydrophilic chromatography enables polar metabolite analysis...
Recent advances in nucleic acid sequencing now permit rapid and genome-scale analysis of genetic variation transcription, enabling population-scale studies human biology, disease, diverse organisms. Likewise, mass spectrometry proteomics highly sensitive accurate protein expression at the whole proteome-scale. However, most proteomic rely on consensus databases to match spectra peptide sequences, thus remain limited canonical sequences. Here, we develop ProteomeGenerator2 (PG2), based...
Cross-linking mass spectrometry (XL-MS) provides low-resolution structural information to model protein structures. Here, we present a protocol identify cross-links of purified antibody binding human leukocyte antigen (HLA). We describe steps for using discovery-based XL-MS approach followed by targeted approach. then detail procedures the identified with other data molecular docking HLA. This has applications modeling interacting structure antigen. For complete details on use and execution...
Repair of critical-size articular cartilage defects typically involves delivery cells in biodegradable, 3D matrices. Differences the developmental status mesenchymal stem (MSCs) and terminally differentiated mature chondrocytes might be a critical factor engineering appropriate matrices for tissue engineering. This study examined relationship between material-driven early cell morphological adaptations chondrogenic outcomes, by studying influence aligned collagen type I (Col I) presentation...
Abstract Severe dengue infections are characterized by endothelial dysfunction shown to be associated with the secreted nonstructural protein 1 (sNS1), making it an attractive vaccine antigen and biotherapeutic target. To uncover biologically relevant structure of sNS1, we obtained infection-derived sNS1 (isNS1) from DENV-infected Vero cells through immunoffinity purification instead recombinant (rsNS1) overexpressed in insect or mammalian cell lines. We found that isNS1 appeared as...
Recent advances in nucleic acid sequencing now permit rapid and genome-scale analysis of genetic variation transcription, enabling population-scale studies human biology, disease, diverse organisms. Likewise, mass spectrometry proteomics highly sensitive accurate protein expression at the whole proteome-scale. However, most proteomic rely on consensus databases to match spectra peptide proteins sequences, thus remain limited canonical sequences. Here, we develop ProteomeGenerator2 (PG2),...
Alloantibody recognition of donor human leukocyte antigen (HLA) is associated with poor clinical transplantation outcomes. However, the molecular and structural basis for alloantibody-HLA interaction not well understood. Here, we used a hybrid modeling approach on previously studied interacting pair inputs from ab initio, in silico, vitro data. Highly reproducible cross-linking mass spectrometry data were obtained both discovery- targeted spectrometry-based approaches approaches. The...
Severe dengue infections are characterized by endothelial dysfunction shown to be associated with the secreted nonstructural protein 1 (sNS1), making it an attractive vaccine antigen and biotherapeutic target. To uncover biologically relevant structure of sNS1, we obtained infection-derived sNS1 (isNS1) from DENV-infected Vero cells through immunoffinity purification instead recombinant (rsNS1) overexpressed in insect or mammalian cell lines. We found that isNS1 appeared as approximately 250...